I also figured it was like the Ren incident in Tsukihime; as in, Rider projecting a very realistic dream into his mind. Ren actually didn't sleep with Shiki until she made a contract as his familiar in Kagetsu Tohya.

Hmm... not exactly. As I got it, Len projected some dream into Shiki's brain or something, not being nailed by Shiki. Rider did have sex with Shirou to replenish her magical stuff and be less of a burden to Sakura. Again, that's how I got it.

I figured it was a misinterpretation of Sakura's command to protect Shirou. In the same way Arc gives Shiki a totally inappropriate reward. LOL.

Anyway, what's so wrong of being raped by sultry woman? I see no wrong there!